AMBER Archive (2009)

Subject: Re: [AMBER] Trying to patch amber 9

From: Jack Shultz (js_at_drugdiscoveryathome.com)
Date: Wed Jun 24 2009 - 10:18:23 CDT

I did this about a year ago on cygwin when I first got Amber9. So I'm
surprised I have this error now.

On Wed, Jun 24, 2009 at 10:58 AM, case <case_at_biomaps.rutgers.edu> wrote:

> On Wed, Jun 24, 2009, Jack Shultz wrote:
> >
> > $ patch -p0 -N -r patch_rejects < bugfix.all
> > patching file `src/ptraj/ptraj.c'
> > Assertion failed: hunk, file patch.c, line 321
>
> This appears to be some problem with patch, not with our files. Do a
> "which
> patch" to make sure you are running the correct executable.

$ which patch
/cygdrive/c/unix_utils/usr/local/wbin/patch

> What OS are you
> using?

cygwin

> It's possible that line endings in the patch file might not match your
> system -- use a text editor to be sure that the bugfix.all file looks OK.
>

as far as I can tell the bugfixall looks fine.
maybe version of patch???

jshultz_at_Hydrogen /usr/local/amber9
$ patch -v
patch 2.5
Copyright 1988 Larry Wall
Copyright 1997 Free Software Foundation, Inc.

This program comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of this program
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING.

written by Larry Wall with lots o' patches by Paul Eggert

>
> Even with bad input, patch should not exit with an assertion failure. And,
> I
> just re-verified that the patch file for Amber9 works fine for me. So
> something weird is happening here.
>
> ...dac
>
>
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> 

-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org

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